https://github.com/nci-gdc/vep-cwl

GDC VEP Variant Annotation Workflow
https://github.com/nci-gdc/vep-cwl

bioinformatics cwl workflow

Last synced: 6 days ago
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GDC VEP Variant Annotation Workflow

• Host: GitHub
• URL: https://github.com/nci-gdc/vep-cwl
• Owner: NCI-GDC
• License: apache-2.0
• Created: 2016-03-31T14:49:01.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2024-04-16T19:08:18.000Z (9 months ago)
• Last Synced: 2024-04-16T23:47:47.125Z (9 months ago)
• Topics: bioinformatics, cwl, workflow
• Language: Common Workflow Language
• Homepage:
• Size: 124 KB
• Stars: 0
• Watchers: 10
• Forks: 3
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        
# GDC VEP Annotation Workflow

![Version badge](https://img.shields.io/badge/VEP-v84-.svg)

![Version badge](https://img.shields.io/badge/VEP-v102-.svg)

This workflow takes a VCF file and adds [Variant Effect Predictor](http://useast.ensembl.org/info/docs/tools/vep/index.html)

annotations using particular settings for the GDC harmonization process.

## Notes

* Tested on [cwltool](https://github.com/common-workflow-language/cwltool) version `1.0.20180306163216`

* See [GDC Reference Files](https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files)

* Plugins and Dockerfile available at https://github.com/NCI-GDC/vep-tool

* Currently, we are using VEP v84 with our customized cache file (see [VEP-SETUP.md](VEP-SETUP.md) for more information) or v102.